The Conformational Free-Energy Landscape of β-d-Mannopyranose: Evidence for a1S5→ B2,5→OS2Catalytic Itinerary in β-Mannosidases

2010 ◽  
Vol 132 (45) ◽  
pp. 16058-16065 ◽  
Author(s):  
Albert Ardèvol ◽  
Xevi Biarnés ◽  
Antoni Planas ◽  
Carme Rovira
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Conformational Free Energy

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2019 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Materials Synthesis ◽  
Factors Affecting ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermostructural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of MOF structure defects during synthesis. In this paper, we evaluate factors affecting the flexibility of MIL-101(Cr) half – secondary building units (half-SBUs) in solution using enhanced sampling methods. In particular, we calculate entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs, in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). We find that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, we investigate the role of enthalpy and entropy in the conformational rearrangement of an SBU in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. Our analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units, as such effects can significantly impact the relative stability of structurally different conformers, which ultimately can be responsible for the formation of defects during materials synthesis.

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2019 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Materials Synthesis ◽  
Factors Affecting ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermostructural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of MOF structure defects during synthesis. In this paper, we evaluate factors affecting the flexibility of MIL-101(Cr) half – secondary building units (half-SBUs) in solution using enhanced sampling methods. In particular, we calculate entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs, in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). We find that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, we investigate the role of enthalpy and entropy in the conformational rearrangement of an SBU in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. Our analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units, as such effects can significantly impact the relative stability of structurally different conformers, which ultimately can be responsible for the formation of defects during materials synthesis.

scholarly journals On the Role of Enthalpic and Entropic Contributions to the Conformational Free Energy Landscape of MIL‐101(Cr) Secondary Building Units

2020 ◽  
Vol 3 (12) ◽  
pp. 2000092
Author(s):  
Loukas Kollias ◽  
David C. Cantu ◽  
Vassiliki‐Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Secondary Building Units ◽  
Conformational Free Energy

scholarly journals The Effect of Tensile Stress on the Conformational Free Energy Landscape of Disulfide Bonds

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e108812 ◽  
Author(s):  
Padmesh Anjukandi ◽  
Przemyslaw Dopieralski ◽  
Jordi Ribas–Arino ◽  
Dominik Marx
Keyword(s):  
Free Energy ◽  
Tensile Stress ◽  
Disulfide Bonds ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Conformational Free Energy

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2020 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Factors Affecting ◽  
Secondary Building Units ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermo-structural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of defects in MOF structures during synthesis. In this paper, factors affecting the flexibility of MIL-101(Cr) half-secondary building units (half-SBUs) are evaluated in solution using enhanced sampling methods. In particular, entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs are calculated in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). This analysis leads to the observation that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, the role of enthalpy and entropy in the conformational rearrangement of an SBU is investigated in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. This analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units and highlights the significant impact they have on the relative stability of crystal-like and non-crystal-like conformers.

scholarly journals The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases

2015 ◽  
Vol 6 (2) ◽  
pp. 1167-1177 ◽  
Author(s):  
Javier Iglesias-Fernández ◽  
Lluís Raich ◽  
Albert Ardèvol ◽  
Carme Rovira
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Energy Landscapes ◽  
Free Energy Landscapes ◽  
Dynamics Simulations ◽  
Conformational Free Energy

Ab initio conformational free energy landscapes, together with molecular dynamics simulations, enable to predict the catalytic itineraries of β-xylanase enzymes.

scholarly journals On the Role of Enthalpic and Entropic Contributions on the Conformational Free Energy Landscape of MIL-101(Cr) Structural Building Units

2020 ◽  
Author(s):  
Loukas Kollias ◽  
David Cantu ◽  
Vassiliki-Alexandra Glezakou ◽  
Roger Rousseau ◽  
Matteo Salvalaglio
Keyword(s):  
Free Energy ◽  
Metal Organic Framework ◽  
Energy Landscape ◽  
Ionic Species ◽  
Free Energy Landscape ◽  
Factors Affecting ◽  
Secondary Building Units ◽  
Enthalpy And Entropy ◽  
Conformational Free Energy

The thermo-structural behavior of metal-organic framework (MOF) precursors is responsible for regulating the introduction of defects in MOF structures during synthesis. In this paper, factors affecting the flexibility of MIL-101(Cr) half-secondary building units (half-SBUs) are evaluated in solution using enhanced sampling methods. In particular, entropic and enthalpic contributions to the conformational free energy landscape of isolated MIL-101(Cr) half-SBUs are calculated in water, in the presence and absence of ionic species (Na<sup>+</sup> and F<sup>-</sup>), and in N, N-dimethylformamide (DMF). This analysis leads to the observation that the interplay between enthalpy and entropy determines the most probable conformational state for half-SBUs. Furthermore, the role of enthalpy and entropy in the conformational rearrangement of an SBU is investigated in water, noting that entropic contributions are essential to stabilize configurations that depart from those coherent with the MIL-101(Cr) crystal structure. This analysis highlights the importance of explicitly considering entropic effects on the configurational ensembles of MOF building units and highlights the significant impact they have on the relative stability of crystal-like and non-crystal-like conformers.

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